SMTL ID : 8h9p.1

Human ATP synthase F1 domain, state 3b

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain A: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, Q.432 Chain F: H.331, R.359 Ligands: MG.2 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:Q.172, A:T.173, A:T.173, A:G.174, A:K.175, A:T.176, A:S.177, A:S.177, A:Q.430, A:Q.432 Salt bridges: A:K.175, A:K.175, F:H.331, F:R.359, F:R.359 ATP.3: 16 residues within 4Å: Chain B: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, G.431, Q.432 Chain D: R.359, D.362 Ligands: MG.4 15 PLIP interactions: 4 interactions with chain D, 11 interactions with chain B Hydrogen bonds: D:R.359, D:R.359, D:D.362, B:Q.172, B:T.173, B:G.174, B:K.175, B:T.176, B:S.177, B:S.177, B:Q.430, B:Q.432 Salt bridges: D:R.359, B:K.175, B:K.175 ATP.5: 14 residues within 4Å: Chain C: Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, Q.432 Chain E: R.359, Y.371 Ligands: MG.6 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:T.176, C:S.177, C:S.177, C:Q.430, C:Q.432, E:R.359 Salt bridges: C:K.175, C:K.175 pi-Stacking: C:F.357

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.176 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.176 MG.4: 4 residues within 4Å: Chain B: T.176, Q.208, D.269 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.176 MG.6: 3 residues within 4Å: Chain C: T.176, D.269 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.176 MG.8: 4 residues within 4Å: Chain E: T.166, E.191, D.259 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.166 MG.10: 5 residues within 4Å: Chain F: N.260, I.261, F.262, A.312 Ligands: ADP.9 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.7: 16 residues within 4Å: Chain B: V.371, R.373 Chain E: G.160, G.162, V.163, G.164, K.165, T.166, V.167, R.192, Y.348, F.421, A.424, F.427, T.428 Ligands: MG.8 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain E Hydrogen bonds: B:R.373, E:G.162, E:V.163, E:G.164, E:K.165, E:T.166, E:T.166, E:V.167 Salt bridges: B:R.373, B:R.373, E:K.165, E:R.192 pi-Stacking: E:Y.348 ADP.9: 14 residues within 4Å: Chain C: R.373 Chain F: G.156, L.157, F.158, G.159, G.160, G.162, K.165, E.195, N.260, Q.311, A.312, L.332 Ligands: MG.10 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:K.165, F:E.195, C:R.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lai, Y. et al., Structure of the human ATP synthase. Mol.Cell (2023)

Release Date

2023-05-31

Peptides

ATP synthase subunit alpha, mitochondrial: ABC
ATP synthase subunit beta, mitochondrial: DEF
ATP synthase subunit gamma, mitochondrial: G
ATP synthase subunit O, mitochondrial: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
D

G
G

H
O

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta, mitochondrial

ATP synthase subunit gamma, mitochondrial

ATP synthase subunit O, mitochondrial

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